Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012200.1 Corchorus olitorius cultivar O-4 contig12233, whole genome shotgun sequence

Parameters: 2 7 7 80 10 50 1000

Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000

Length: 5797
ACGTcount: A:0.33, C:0.21, G:0.16, T:0.30


Found at i:1130 original size:50 final size:50

Alignment explanation


    Indices: 1075--1175  Score: 166
    Period size: 50  Copynumber: 2.0  Consensus size: 50

       1065 GAGATTTTAT

                       *               *              *   *   
       1075 AATAAGATTGCTTTCCATTTGTGAGTCTAAGATCAAAATTCGCTTTTCAA
          1 AATAAGATTGCATTCCATTTGTGAGTCCAAGATCAAAATTCGATTTCCAA

                                                              
       1125 AATAAGATTGCATTCCATTTGTGAGTCCAAGATCAAAATTCGATTTCCAA
          1 AATAAGATTGCATTCCATTTGTGAGTCCAAGATCAAAATTCGATTTCCAA

             
       1175 A
          1 A

       1176 GGGCATTTTA


Statistics
Matches: 47,  Mismatches: 4, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  50   47  1.00

ACGTcount: A:0.35, C:0.17, G:0.14, T:0.35


Consensus pattern (50 bp):   
AATAAGATTGCATTCCATTTGTGAGTCCAAGATCAAAATTCGATTTCCAA

Found at i:1883 original size:68 final size:68

Alignment explanation


    Indices: 1769--1927  Score: 246
    Period size: 68  Copynumber: 2.3  Consensus size: 68

       1759 AGATTTTGCC

                          *  *                     *                   *     
       1769 TGGTTCCATCCAAGAAGAAGGGGCTTTCTCACAAGCCAACCCCGTTTCCATACGAGCCAGTTAAG
          1 TGGTTCCATCCAAGCAGCAGGGGCTTTCTCACAAGCCAAACCCGTTTCCATACGAGCCACTTAAG

               
       1834 CCT
         66 CCT

                                                     *              *     *  
       1837 TGGTTCCATCCAAGCAGCAGGGGCTTTCTCACAAGCCAAACTCGTTTCCATACGAGTCACTTGAG
          1 TGGTTCCATCCAAGCAGCAGGGGCTTTCTCACAAGCCAAACCCGTTTCCATACGAGCCACTTAAG

               
       1902 CCT
         66 CCT

                            *      
       1905 TGGTTCCATCCAAGCAACAGGGG
          1 TGGTTCCATCCAAGCAGCAGGGG

       1928 ATTTTCTGAT


Statistics
Matches: 83,  Mismatches: 8, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  68   83  1.00

ACGTcount: A:0.25, C:0.30, G:0.22, T:0.23


Consensus pattern (68 bp):   
TGGTTCCATCCAAGCAGCAGGGGCTTTCTCACAAGCCAAACCCGTTTCCATACGAGCCACTTAAG
CCT

Found at i:2759 original size:21 final size:21

Alignment explanation


    Indices: 2735--2847  Score: 158
    Period size: 21  Copynumber: 5.4  Consensus size: 21

       2725 CTTAGGCATT

                         *       
       2735 TCCAATGAGCTTGAAACCTTC
          1 TCCAATGAGCTTGGAACCTTC

                    *            
       2756 TCCAATGATCTTGGAACCTTC
          1 TCCAATGAGCTTGGAACCTTC

                    *          * 
       2777 TCCAATGAACTTGGAACCTGC
          1 TCCAATGAGCTTGGAACCTTC

                                  
       2798 TCCAATGAGCTTGGAA-CTTGC
          1 TCCAATGAGCTTGGAACCTT-C

                                  
       2819 TCCAATGAGCTTGGAA-CTTGC
          1 TCCAATGAGCTTGGAACCTT-C

                    
       2840 TCCAATGA
          1 TCCAATGA

       2848 ACTTCTAGCA


Statistics
Matches: 85,  Mismatches: 6, Indels: 2
        0.91            0.06        0.02

Matches are distributed among these distances:
  20    2  0.02
  21   83  0.98

ACGTcount: A:0.27, C:0.27, G:0.19, T:0.28


Consensus pattern (21 bp):   
TCCAATGAGCTTGGAACCTTC

Found at i:4722 original size:33 final size:33

Alignment explanation


    Indices: 4652--4793  Score: 132
    Period size: 33  Copynumber: 4.3  Consensus size: 33

       4642 ATGATCAACC

                                     ** *      
       4652 AAAACAGATTT-GTTTTCATCACAATTAGCATCC-
          1 AAAACAGATTTAG-TTTCATCACAAACAACA-CCT

                                              
       4685 AAAACAGAATTT-GTTTCATCACAAACAACACCT
          1 AAAACAG-ATTTAGTTTCATCACAAACAACACCT

                          *                  
       4718 AAAACAGATTTAGTGTCATCACAAACAACA-CT
          1 AAAACAGATTTAGTTTCATCACAAACAACACCT

                **  *      *               *  
       4750 CAAATTAGGTTTAGTATCATCAC-AACAACATCT
          1 -AAAACAGATTTAGTTTCATCACAAACAACACCT

                       
       4783 AAAACAGATTT
          1 AAAACAGATTT

       4794 TTGCACAATT


Statistics
Matches: 93,  Mismatches: 11, Indels: 11
        0.81            0.10        0.10

Matches are distributed among these distances:
  32   23  0.25
  33   65  0.70
  34    5  0.05

ACGTcount: A:0.43, C:0.21, G:0.08, T:0.27


Consensus pattern (33 bp):   
AAAACAGATTTAGTTTCATCACAAACAACACCT
Done.